Pangenomics
Table of Contents
Find below each resource tagged with pangenomics. You can also go back to see all resources.
Tutorials and exercises
Tutorials are the best way to start learning anvi’o. They typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi’o often with hands-on experience (add more here).
A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course.
A hands-on tutorial to learn how to integrate single-cell genomics data. It covers functional and taxonomic assignment, pangenomic and phylogenomic analyses, and more.
A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.
Using publicly available genomes and metagenomes, and anvi'o build in snakemake workflow to contextualize a genome of interest.
Technical write-ups
Articles listed this section offer solutions or discussions regarding matters that are typically more technical than scientific (add more here).
A tutorial that will walk you through the steps of downloading genomes of interest from the NCBI, processing NCBI GenBank files to get anvi’o compatible files, and running the anvi’o snakemake workflow for contigs to generate a contigs database for each of these genomes.
Demonstration of a way to incorporate new genomes with reference genomes from NCBI, while maintaining their vetted reference-genome annotations.
A workflow to demonstrate how to import AGNOSTOS gene categories into anvi'o databases
Articles, workflows, opinions
These resources often cover key insights into specific topics and can be useful to more advanced users and ‘omics enthusiasts in general (add more here).
An application of metagenomic long-read sequencing, assembly, correction, and the use of anvi'o pangenomics workflow to benchmark outcomes.
A diary that shed light on the story and purpose of AGNOSTOS.
Developer and contributor resources
Here you will find technical documentation to help you learn how to contribute to anvi’o, as a developer or otherwise (add more here).
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